Section: New Software and Platforms


Exhaustive Rotational Search using Branch-and-Bound algorithm for rigid docking

Keywords: 3D modeling - Proteins - Docking

Functional Description: EROS-DOCK is a protein-protein docking program for Linux. It takes in input the 3D structures of two proteins in PDB format, and gives as output a list of transformation matrices describing the most probable relative positions of the two proteins in nature, together with a score (approximation of their binding energy for that position). On a modern workstation, docking times is in the order of few hours for a blind global search. The user can also provide nowledge of particular contact points at the surface of each protein, which accelerates the pruning of the solutions space. The underlying algorithm uses a pi-ball representation of the rotational 3D space, to accelerate the search for close-fitting orientations of the two molecules by a branch-and-bound technique.